I think its a combination of two things.
Villanova has been more consistent than KU over the course of the full season. Like KU, they lost 3 of 6 during a stretch, but KU had a separate 2 game losing streak. So over the course of the season, you could argue that Villanova was the better team.
Villanova has played better during the tournament. No one has played Villanova within single digits yet during the tournament. KU has won their last three games by 4 points each.
So if you think Villanova had the slightly better regular season, and you also think Villanova is playing more dominantly right now, Villanova is the pick to win this game. Doesn’t mean KU can’t win. Just that this game, as @LSH says, probably favors the Wildcats.